Software

Biostatistics

Compare Groups of Growth Curves
Compare Groups of Growth Curves performs a permutation test of the difference
between two groups of growth curves. It calculates all pairwise
comparisons between two or more groups of growth curves.

Gene Mapping and Linkage

Linkdatagen
*updated July 2011*
Performs QC and generates
output formats from many common Affymetrix and Illumina SNP chips, as well
as NGS/MPS data. Output formats include MERLIN, ALLEGRO, PLINK, MORGAN,
FEstim and PREST. Different HAPMAP populations can be chosen as
the source of marker allele frequencies.

Age of mutation estimation
R Shiny app, also available as the original R script which performs the calculations required to produce mutation age
estimates and confidence intervals using the method described in
Gandolfo, L. C., Bahlo, M., and Speed, T. P. (2014). Dating rare mutations from
small samples with dense marker data. Genetics, 197(4): 1315-27.

Next-Gen Sequencing

GOseq
An R library for performing Gene Ontology (GO) and other category based tests on
RNA-seq data, which corrects for selection bias.

Subread and Subjunc (R versionC version)
Subread is a general-purpose read aligner (mapping both gDNA- and RNA-seq reads).
It is espeically powerful in mapping RNA-seq reads for the purpose of expression analysis.
Subjunc is designed to discover exon-exon junctions from using RNA-seq data.
It performs full alignments for RNA-seq reads.

Sequence Analysis

GABOS/GAFEP Get ABit Of Sequence/Get AFew Exon Primers.
GABOS retrieves sequence for Exons, Introns, 5'UTRs, CDS, 3'UTRs, Transcripts, Genomic Sequence
and DNA between any two co-ordinates. Sequence can be specified by a list of gene names, or by
selecting all genes within a chromosomal co-ordinate range. Additional up or down stream sequence
maybe specified or sequence maybe limited by base number range within an object (For eg. first 50
bases of each exon). 10 genomes are available, others can be requested. Gene definitions are taken from UCSC defined
sets like refGene, Ensembl genes, MGC genes, Repeat Sequences, EST's, mRNA, STS's etc.
GAFEP will retrieve primers created by Primer3 around exons and introns selected by GABOS. Large
exons/introns will be split to optimum size blocks and small ones will be padded out with adjacent
sequence.

SOCRATES
Socrates is a pure split read-based breakpoint caller, which is designed to be fast and sensitive.
It is a highly efficient for detecting genomic rearrangements in tumours, but requires significant downstream filtering by the user.
SOCRATES is available via Github.
If you find SOCRATES useful, please cite the SOCRATES publication:
Schroeder J, Hsu A, Boyle SE, MacIntyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT.
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Bioinformatics 2014, 30:8, 1064-1072.
Many of the ideas of SOCRATES have now been re-implemented and extended in GRIDSS.

GRIDSS - Genomic Rearrangement IDentification Software Suite
GRIDSS a modular software suite containing tools useful for the detection genomic rearrangements.
GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for i
Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn
graph genome-wide break-end assembly, split read, and read pair evidence.
GRIDSS won the ICGC/TCGA Dream Mutation Calling Challenge #5 SV Sub-challenge in 2015 and
is highest ranked as a late entry in the 2014 challenge.
GRIDSS is described in a preprint
and currently under review.
GRIDSS is available from Github.